3VLF | pdb_00003vlf

Crystal structure of yeast proteasome interacting protein

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Hsm3_like	e3vlfC2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Hsm3_like	ECOD (1.6)
A	RNAse_Pc_like,Hsm3_like	e3vlfA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: RNAse_Pc_like,Hsm3_like	ECOD (1.6)
B	PRK03992	e3vlfB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PRK03992	ECOD (1.6)
D	PRK03992	e3vlfD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PRK03992	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.25.10.50	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant		CATH (4.3.0)
C	1.25.40.580	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.25.10.50	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant		CATH (4.3.0)
A	1.25.40.580	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF18795	DNA mismatch repair protein HSM3, N terminal domain (HSM3_N)	DNA mismatch repair protein HSM3, N terminal domain	-	Repeat
A, C	PF18794	DNA mismatch repair protein HSM3, C terminal domain (HSM3_C)	DNA mismatch repair protein HSM3, C terminal domain	-	Repeat
B, D	PF17862	AAA+ lid domain (AAA_lid_3)	AAA+ lid domain	This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	DNA mismatch repair protein HSM3	protein folding chaperone	cellular component organization cellular component biogenesis proteasome assembly cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis proteasome regulatory particle assembly cellular response to stimulus mismatch repair response to stimulus primary metabolic process DNA metabolic process cellular component organization cellular component biogenesis proteasome assembly cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis proteasome regulatory particle assembly cellular response to stimulus mismatch repair response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B, D	26S protease regulatory subunit 7 homolog	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding proteasome-activating activity	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process regulation of cellular process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process regulation of cellular process transcription preinitiation complex assembly positive regulation of macromolecule biosynthetic process regulation of primary metabolic process cellular component biogenesis nucleobase-containing compound metabolic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process cellular component assembly transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter regulation of transcription by RNA polymerase II regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process regulation of gene expression biosynthetic process RNA polymerase II preinitiation complex assembly regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process regulation of RNA polymerase II transcription preinitiation complex assembly positive regulation of cellular component organization regulation of cellular component organization positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process cellular component organization protein-DNA complex organization RNA biosynthetic process nucleic acid biosynthetic process positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly positive regulation of biosynthetic process protein-containing complex assembly cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of RNA polymerase II transcription preinitiation complex assembly protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of transcription initiation by RNA polymerase II biological regulation protein-DNA complex assembly regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression regulation of cellular component biogenesis macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II positive regulation of protein metabolic process regulation of protein metabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process proteasome assembly proteasome regulatory particle assembly proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process	protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex intracellular anatomical structure proteasome regulatory particle proteasome accessory complex cellular anatomical structure proteasome regulatory particle, base subcomplex cytoplasm membrane-bounded organelle intracellular organelle protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex intracellular anatomical structure proteasome regulatory particle proteasome accessory complex cellular anatomical structure proteasome regulatory particle, base subcomplex cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR041335	DNA mismatch repair protein HSM3, N-terminal domain	Domain
A, C	IPR016024	Armadillo-type fold	Homologous Superfamily
A, C	IPR040752	DNA mismatch repair protein HSM3, C-terminal domain	Domain
B, D	IPR048723	26S proteasome regulatory subunit 7-like, OB domain	Domain
B, D	IPR050221	26S Proteasome Regulatory ATPase	Family
B, D	IPR041569	AAA ATPase, AAA+ lid domain	Domain
B, D	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
B, D	IPR003593	AAA+ ATPase domain	Domain
B, D	IPR003959	ATPase, AAA-type, core	Domain
B, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
B, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.